Merge pull request #111 from OpenSourceBrain/test_jnml

Use pip install for netpyne

Author: pgleeson

.github/workflows/ci.yml

@@ -37,7 +37,7 @@ jobs:
           - PyLEMS
           - PyLEMS_NeuroML2
           - jLEMS
-          - jNeuroML
+          - "jNeuroML:v0.12.2"
           - jNeuroML_Brian2
           - jNeuroML_EDEN
           - "jNeuroML_NEURON:8.2.1"

omv/engines/getjnml.py

@@ -4,10 +4,13 @@
 from pathlib import Path
 
 from omv.engines.utils.wdir import working_dir
+from omv.common.inout import inform
 
 
-def install_jnml():
-    version = "v0.12.2"
+def install_jnml(version):
+
+    if not version:
+        version = "v0.12.2"
 
     try:
         jnmlhome = os.environ["JNML_HOME"]
@@ -41,3 +44,5 @@ def install_jnml():
             ]
         )
         check_output(["unzip", "jNeuroML.zip"])
+
+    inform("Successfully installed jNeuroML "+version, indent=1)

omv/engines/getnetpyne.py

@@ -47,6 +47,6 @@ def install_netpyne(version=None):
                         "python-dateutil==2.8.0",
                     ]
                 )
-            print(check_output([sys.executable, "setup.py", "install"]))
+            pip_install(".")
 
         m = "Successfully installed NetPyNE..."

omv/engines/jneuroml.py

@@ -78,8 +78,8 @@ def is_installed():
     def install(version):
         from omv.engines.getjnml import install_jnml
 
-        inform("Will fetch and install the latest jNeuroML jar", indent=2)
-        install_jnml()
+        inform("Will fetch and install jNeuroML jar", indent=2)
+        install_jnml(version)
 
     def run(self):
         try:

omv/omv_util.py

@@ -226,14 +226,9 @@ def _install_engine(eng):
             if ee.is_installed():
                 already_installed = True
             else:
-                if engine_version is not None:
-                    raise Exception(
-                        "Currently, cannot install a specific version of engine %s"
-                        % eng
-                    )
                 from omv.engines.getjnml import install_jnml
 
-                install_jnml()
+                install_jnml(engine_version)
 
         elif eng.lower() == "neuroConstruct" or eng == "Py_neuroConstruct".lower():
             from omv.engines.pyneuroconstruct import PyneuroConstructEngine as ee